We have applied quantitative scanning transmission electron microscopy (STEM) and energy-filtered transmission electron microscopy (EFTEM) to elucidate the molecular organization of amyloid proteins involved in Azheimers Disease and type 2 diabetes. In Alzheimer's disease, abnormal deposits of amyloid beta protein (Ab) in the brain occur as fibrils within the cerebral neuropil. To characterize the way in which these fibrils assemble under different pH conditions, we have performed scanning transmission electron microscopy (STEM) on synthetic full-length Ab peptides as well as various Ab peptides with truncated sequences. STEM analysis of unstained preparations provides a quantitative determination of the mass-per-length (MPL) and thus the numbers of beta-sheets within fibrils. We have also investigated the use of inelastic dark-field imaging in the energy-filtering transmission electron microscope (EFTEM) as an alternative approach to determining the MPL of amyloid fibrils. Images were collected with an incident electron energy of 300 keV, and energy losses in the range 15 to 35 eV, which corresponds to the broad plasmon resonance for protein. The inelastic EFTEM mass maps were found to be of comparable quality to the STEM mass maps in terms of the signal to noise ratio, but the EFTEM images could be acquired more rapidly. In general, MPL measurements reveal the existence of fundamental fibrillizing units, or "protofilaments," consisting of well-defined numbers of cross-beta sheets. Specifically, we have found twisted fibrils that contain three beta sheets, whose structure has been correlated with atomic-level information about the peptide backbone conformation by our collaborators in NIDDK using NMR spectroscopy. We have also performed mass measurements on amylin peptide, which is the main component of amyloid that develops in the pancreas of type 2 diabetes patients. Amylin readily forms amyloid fibrils in vitro that exhibit a morphology corresponding to a striated ribbon. We have performed STEM mass measurements to show that the basic unit in these protofilament structures contains four layers of parallel beta-sheets, formed by two symmetric layers of amylin molecules. The molecular structure of amylin protofilaments in the striated ribbons closely resembles that found in Alzheimers beta-amyloid fibrils.